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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5.4.19.2.2.3 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.
5.4.19.2.2.4 Interactive Registration
Interactive Registration allows to register the
recoreded views of an experiment manually, when
the other alignment options fail for that dataset
(Fig. 528). The views of one channel at one time
point of the experiment are the basis for the
procedure. The z-stacks of the individual views are
rotated based on the rotation information of the
files meta data and transformed into channels
resulting in one maximum intensity projection
image. Within this newly generated image the
views, now behaving as channels, can be moved in
x, y, z and rotated to overlay each other. When all
views are layed on top of each other, the
Apply
button will use the adjusted parameters to register,
and when required fuse, the views for all time
points of the experiment. An .xml file is created
which can be used for the
Use registration from
file option. This .xml file can be found along with
the processed data in the Result folder.
The first step is to chose the
Registration
Channel that should be used to manually overlay
all views of the experiment by pressing the
according button, e.g.
Cam1 . Only one channel
can be used for this procedure, all other channels
will not be diplayed. If the experiment consists of a
time series, one time point is selected with the
Time slider and spin box of the image controal
area
. This chosen time point is indicated in the
Current Time Point box (Fig. 528).
Fig. 528 Registration Options: Interactive
Registration