Zeiss LSM 880 Operating Manual page 361

LSM 880
If the Fit check box is ticked and the Input 2
checkbox inactive, than the software will align all
channels of Input image having the same format
to the first listed channel of the same format.
Care should be taken about what channels
will be aligned and in which order they
appear. For SIM images the super resolution
(SR) and the widefield (WF) channels are
listed alternatively (pair wise). Since all
channels are of the same format each
channel (SR and WF) would be aligned to
the first SR channel, since SR channels are
normally listed before their corresponding
WF channel. If this should be avoided,
subsets of images containing only SR or WF
channels have to
Processing Tool
independently aligned. The situation is
different for PALM images. The high
resolution (HR) and sum widefield (SWF)
channels are also listed alternatively, with the
HR channels preceding their corresponding
SWF channels, however, the format of the
HR channels is different to the one of the
SWF channels. In this case the software
aligns all HR channels to the first listed HR
channel, which will be the first displayed
channel, and
independently to the first listed SWF
channel, which is second in the list.
With the Fit check box ticked, the coefficient
table lists as the first column the Channel name
Ch and as the last two columns the used Laser line
and camera channel Cam. In between are listed
the corresponding correction coefficients. You
have the choice from the Alignment mode drop
down menu between Lateral, Affine and
Parabolic alignment.
10/2014 V_01
CHAPTER 1 - SYSTEM OPERATION
Left Tool Area and Hardware Control Tools
be created in the
Copy Subset
and
SWF
all channels
000000-2071-464
Fig. 502 Processing Channel Alignment tool
field with one input image (with
SIM and
selected
ZEISS
paired WF channels)
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