Zeiss LSM 880, Operating Manual

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CHAPTER 1 - SYSTEM OPERATION
LSM 880 Left Tool Area and Hardware Control Tools ZEISS
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Ignore Sample
: This option activates an additional function to find structures within the sample that
were incorrectly labeled as beads (fiducials). These structures are not taken into account during the
Landmark Alignment process; but they are not removed from the
Preview .
Expand To Maximum Volume
: This checkbox is activated as default. In a multiview experiment not all
views might include all the information. When Expand To Maximum Volume is activated, the volume
of the resulting dataset after registration and fusion is determined and additional black pixel (x,y) and z-
slices are added to the views during registration. This prevents loss of data for later fusion.
Scaling x=y=z : The dimensions are downsized to the smallest to have the same size. If the scaling in
Deconvolution, PSF settings
(Fig. 520) is changed, the latter will override the scaling settings here.
Individual Registration For Every Time point : If the multiview experiment has been performed over
time, this option becomes available.
−
If activated , each time point generates a transformation matrix and each time point is registered
individually. As a result, the time necessary for registration is multiplied by the number of time
points and can rise substantially. However, if the motorized movement of the sample by the system
has changed (e.g. due to thermic effects on the system: not fully warmed up at start, incubation,
air conditioning of the room), the
Individual Registration For Every Time point option becomes
necessary.
−
If
not activated
, one transformation matrix is generated for all the following time points based on
the first time point. As a result, processing for registration has only to be done once which reduces
processing time.
5.4.19.2.3 Input Settings
In this sub-menu, a subset of a present time series
can be chosen for the Registration and Fusion
processing (Fig. 533).
Use the two sliders or input boxes with arrows on
each side to truncate the
Time
points. If not every
time point in this period should be taken, the
Steps can be defined with the input-box with
arrows.
If a subset of a time series is defined this way, the
resulting images will be numbered according to
their new sequence, which might not be the same
as in the input file.
Fig. 533 Processing – Lightsheet Processing.
Multiview Processing, Input
Settings