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24 – LSM 880 Training Guide
Collecting a Z-Stack
To collect serial sections (Z) we need to first activate the Z-Stack tools in ZEN which are hidden by default.
1.
Check ‘Z-Stack’ from the experiment options. This will activate the Z
Stack dialog in the Multidimensional Acquisition settings.
2.
Click ‘Live’ to begin scanning an actively updated image.
3.
Focus the drive in one direction (does not matter which direction you
start with) until the image of your sample just goes out of focus.
4.
From the Z-Stack dialog, click ‘Set First’ to mark the start position.
5.
While continuing to scan, focus the drive in the opposite direction until
your sample comes back into focus, then continue focusing until it goes
out of focus again. This time on the opposite side of the sample.
6.
Click ‘Set Last’.
7.
Click ‘Optimal’ to set the interval size to be equal to
½
the optical section
thickness.
8.
Click ‘Start Experiment’ to initiate your Z-Stack.
Note: The focus drive will always operate against gravity for maximum
reproducibility. On an inverted microscope, if you mark the point furthest
from the objective as ‘First’ the system will automatically start from ‘Last’ and
go to ‘First’. The opposite is true for an upright microscope.