Zeiss LSM 880 Operating Manual page 366

ZEISS
In either case, the other loaded image does not play a role. In the coefficient table the channel (Ch)
assignment column is replaced by an identity (Id) column that numbers the channels in their ascending
Fig. 514 ID drop down menu
The channel alignment tool is generically programmed to have high flexibility. Care should
therefore be exerted in the control which channels are how aligned as there are no warnings, if
unrelated channels are aligned to each other.
If you draw Regions of Interests (ROIs) in the image, they will be taken for alignemnt. For parabolic fit,
you should have at least 3 well spaced regions. If you have fiducial markers, you can use them by setting
the ROIs around them. Please be aware that in the z-direction the algorithm scans the whole z-Stack and
takes the brightest area in th z-direction. If your beads are not the brightest structure, than the alignment
will fail.
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CHAPTER 1 - SYSTEM OPERATION
Left Tool Area and Hardware Control Tools
order starting with 0.
The assignment table represents the selected image,
either Input image (Input 2 check box inactive) or
Input image 2 (Input 2 check box ticked).
Note that the dimensionality must not be the same as in
the coefficient table. The assignment table lists the
channels (Ch) and the laser lines used (Laser). With the
identity (ID) drop down menu (Fig. 514), an ID from the
coefficient table can be assigned individually to a
channel. That channel will then be corrected exactly with
the coefficients of that ID.
If no alignment should be performed do not align can
be chosen.
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LSM 880
10/2014 V_01