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A Z-stack can be configured in the Acquisition Settings panel. You have the option to reset the current focus position to zero, which you can do by pressing Set 0 (but see the warning below). Focus on the plane where you would like to start the Z-stack and press Set under Start, then focus on the last plane of the stack and press Set under End.
Warning title Warning If you want to reset the focus position to zero, do it before you set the Start and End positions, otherwise the Z series will be many microns out of focus.
Set a Step size in μm by typing in a value or press Op. for the microscope to set the optimal step size for the objective lens currently being used. If the Z-stack menu is hidden just double-click on Microscope to display it. Click Depth beneath the XY button in Image Acquisition Control. The XY button starts the acquisition, but if If Depth is not clicked then only a single XY plane (no Z) will be scannedcaptured when the scan starts. The Lambda, Time, etc. buttons should be activated for spectral scans, time series and other combinations.
- When the Z series is finished you must press Series Done (below) to open a window displaying the Z-stack, which you can then save. Alternatively you can press Append Next to acquire another Z-stack and append it to the previous one, but this is not likely to be a common practice.
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