Zeiss LSM 880 Operating Manual page 362

ZEISS
Fig. 503 Alignment mode drop down
menu for selected PALM
image
Fig. 504 Correction table in the Lateral
alignment mode
Fig. 505 Coefficient table in the Affine
alignment mode
Fig. 506 Coefficient
Parabolic alignment mode
356
CHAPTER 1 - SYSTEM OPERATION
Left Tool Area and Hardware Control Tools
table in the
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Lateral (Fig. 503) is used to correct for linear lateral and
axial drifts, that is in all directions. Linear alignments are
performed in the x, y and z direction, when the Applied
button is pressed. The respective offsets (coefficients) are
displayed in the coefficient table in the X, Y and Z
columns, respectively (Fig. 504).
For SIM, WF and SWF images, the software will use
significant structures for performing the alignment. You
can set a ROI and then the structure within the ROI is
used. For HR (PALM) images at least one fiducial is
expected. Without a fiducial, no alignment will be
performed in this case.
Affine is used to correct for linear lateral (X, Y) and axial
(Z) drifts, rotational offsets in the image plane in x and y
(RX, RY) as well as a 1
plane in x and y (SX, SY). The respective offsets
(coefficients) are displayed in the coefficient table in
the corresponding columns (Fig. 505). The scrollbar can
be used to have access to all columns. For SIM, WF and
SWF images, the software will use significant structures
for performing the alignment. You can set a ROI and
then the structure within the ROI is used. For HR (PALM)
images at least three fiducials are expected. Without
fiducials, no alignment will be performed in this case.
Parabolic is used to correct for linear lateral (X, Y) and
axial (Z) drifts as well as chromatic aberrations, where a
2 nd order stretching in the image plane in x (X1, X2) and
y (Y1, Y2) is performed. The respective offsets
(coefficients) are displayed in the coefficient table in
the corresponding columns (Fig. 506). The scrollbar can
be used to have access to all columns. Parabolic only
works with HR (PALM) images and is displayed only in
the Alignment mode drop down menu, when a HR
(PALM) image is selected as the Input image.
The calculated coefficients in the coefficient table
can be edited by hand. The correction will be
exactly performed when pressing Apply according
to the coefficients in the coefficient table.
If the Save button is pressed, the coefficient
table (with the coefficients) will be saved in a .bin
file. These .bin file can be reloaded by pressing the
Load button via the Windows Explorer. The
Load button becomes only active when the Fit
check box is not active.
st
order stretching in the image
10/2014 V_01
LSM 880