Zeiss Lightsheet Z.1, Руководство по эксплуатации

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CHAPTER 4 - SYSTEM OPERATION
Lightsheet Z.1 Left Tool Area and Hardware Control Tools Carl Zeiss
02/2013 000000-1790-528 151
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.
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
upon the first time point. As a result, processing for registration has only to be done once which
reduces processing time.
Registration Options: Use Registration From File
When the Registration for the dataset has been determined already and the transformation matrix has
been saved as an .xml file (Filename.czi.xml), this option can be chosen. Click on the button next to
Registration File to open a Windows Explorer window in which you can find and select the file.
With the drop down menus, the
Interpolation
mode and
Dual Side Fusion
processing can be chosen
(see as well Landmark Alignment or Intensity Based Alignment section).
Expand To Maximum Volume : This checkbox is activated as the default. In a multiview experiment, the
Z-Stacks are often of different sizes. When
Expand To Maximum Volume
is activated, it will use the
maximum slice number (from one View) present in the dataset for registration. The additional z-slices
needed in other views will be filled with black frames. This will ensure that no data is lost from views with
larger z-dimensions. If this checkbox is not activated, the number of z-slices from the first View is taken
as the default and larger Z-Stacks will be cut; there is a risk of data loss.
Scaling x=y=z
: The dimensions are downsized to the smallest to have the same size.
Input settings
In this sub-menu, a subset of a present time series
can be chosen for the Registration and Fusion
processing (Fig. 236).
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. 236 Processing – Lightsheet Processing.
Multiview Processing, Input Settings