ZEISS
Left Tool Area and Hardware Control Tools
ELYRA 7
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000000-2262-999
03/2019 V_02
In Advanced settings you can check or uncheck the
Histogram Baseline Cut
box to select or deselect
baseline cut with baseline shift being used if the box is not ticked. In
Baseline Shift
negative values that
can arise as an artifact by the
Noise
or Wiener
filter
(
Sharpness
filter) will be kept and an offset is
added to the whole image, so that the minimal (negative) intensity becomes zero intensity. In
Baseline
Cut
negative values will be clipped by setting them to zero. No offset is applied.
DCF
and
WF
check boxes
are available (Fig. 387) that if ticked will compute
in addition to the SIM image the selected
deconvolved (DCV) and widefield (WF) images. For
example, if +WF was ticked the resulting
computed image consists of a
SIM
and
WF
channel (Fig. 388).
If the the
Histogram Scale to Raw Image
is
unchecked, output images will be normalized to
the maximum dynamic range. Please note that in
this case quantitative information is lost, however,
images are displayed with best brightness and
contrast. If you want to keep the original scaling
for quantitative studies, you have to check the
Histogram Scale to Raw Image
box. In this case
the original dynamic range is kept.
You can select between theoretically computed or
experimentally determined PSF by ticking or
unticking the
Experimental
PSF
check box
(Fig. 389). If not checked, the
Theoretical PSF
is
taken. If checked, the Windows explorer
Open
icon becomes available. Pressing the button will
open Windows Explorer, which allows you to select
any pre-saved Experimental PSF. The file name of
the loaded file is displayed in the
PSF File
display
window along with the director path.
Note, if the number of the Experimental PSF channels is less than the number of the WF or SIM
channels, the theoretical PSF will be used for the missing channels and a warning is generated. The
program also checks the match of the excitation wavelengths between the PSF and WF / SIM
channels. In case of mismatching, it generates a warning, but the experimental PSF will still be
used.
In
SIM
processing tool, you have the possibility to also perform a channel alignment after
processing. To this end check the
Channel Alignment
box (Fig. 389) and select a pre-defined
template via Windows Explorer. The file name of the loaded file is displayed in the
Channel
Alignment File
display window along with the directory path.
Fig. 387
DCV and +WF checkboxes
Fig. 388
SIM image (left) and widefield image
(right) in the Split mode after SIM
processing with cWF box
Fig. 389
Selection boxes for Experimental PSF
and Channel Alignment