Performing A Z-Stack Using Center Mode - Zeiss LSM 880 Operating Manual

ZEISS
Fig. 194 Z-Stack tool Center mode with
Z-Stack Navigation displayed for
the LSM image mode
The values for number of Slices and Interval are taken over from any settings done in First/Last mode.
The Offset defines the Center position of the stack in relation to the Focus Position.
The Slices input box displays the number of slices of the stack. This number can be edited by typing or
using the arrow keys. Changing the value for Slices leaves the Interval untouched, but the total Range
is adjusted.
The Interval input box displays the z-distance (interval) between slices in µm. This number can be edited
by typing or using the arrow keys. Changing the value for the Interval automatically adjusts the number
of Slices while adjusting the total Range. The Slices number will remain unchanged.
Pressing the Optimal button sets Interval to match the Nyquist criteria (2 fold over sampling) and
accordingly sets the number of Slices. The optimal interval is displayed in the button in µm.
Within the Keep display field (only available in Show all mode) you have the option to switch between
Keep Interval and Keep Slice. If Keep Interval is checked, the number of slices is adjusted to a new
Range defined pressing Set First or Set Last. Likewise, when Keep Slice is checked, the value for the
Interval between the slices is adjusted to a new Range defined by pressing Set First or Set Last.
The Position (µm) input box indicates the current position of the focus, no matter if the focus drive or a
Z-Piezo stage insert was used for positioning. The arrow keys allow to change the focus in small steps. If
the Use Piezo check box is ticked (only available, if a Z-Piezo stage is attached to the system), the Z-
Piezo stage insert will be used to perform all Z movements triggered from the software. If the focus drive
was used for Set First / Set Last, the system will transform this numbers for a matched Z-Piezo
movement.
The Fast Z Line checkbox is only available in LSM imaging mode and only Line Scan Mode to be
selected in the Acquisition Mode tool. It is not possible with the Z-Piezo. If the check box is ticked and
Continuous action button pressed a fast XZ scan for overviews is performed using a continuous
movement of the microscope focus. The stack size is retained and the interval is adapted depending on
the scan speed.
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CHAPTER 1 - SYSTEM OPERATION
Left Tool Area and Hardware Control Tools
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5.2.15.2 Performing a Z-Stack Using Center
Mode
Press the Center mode button to open the Center
definition panel (Fig. 194). This mode allows
setting the Range of the Z-Stack in relation to the
current Focus Position which is indicated as
Offset.
In addition it is possible in the LSM imaging
mode to use the image of a XZ scan (line scan in
Z) for positioning the Z-Stack range. This tool sets
the first and last slice symmetrically in relation to a
defined Center position. One should have an idea
about the size of the stack when using this mode.
It is useful when several Z-Stacks of the same
range should be acquired at different positions
within the specimen, as the whole range of the
stack can be set to a different position at once
using the Offset function.
LSM 880
10/2014 V_01