Manual processing
If SIM artifacts and aberrations are visible in the processed image, fine tuning with manual
processing can help to eliminate the problems.
During the SIM introduction we discuss the parameters and how to find/remove artifacts in more
details.
For the best results acquire always a small Z-stack (use Center mode) with around 5 planes with
optimal section intervals. With this small focus drifts can be also avoided.
Don’t forget to save the file after acquisition and after processing. Use .czi format and if you need,
export the image as .tiff.
Fourier space
(dummy, not
from the exact dataset, but
good for checking the effect
of the different settings)
First check what parameters
were used for automatic
processing under the
info tab
.
Noise filter
has the biggest
effect in changing the
resolution and removing
artifacts
Baseline shifted/cut
:
Background values for the
histogram. “Shift” keeps
everything, “cut” contrasts,
removes background
Switch to
manual
processing
to change parameters
Select the planes to process
(single plane or first-last)
If it is a Z-stack, select
3D
Uncheck Auto noise filter
and change the Noise filter
parameter. If the automatic
processing was -6, try to
decrease the resolution to -5,
-4, etc till SIM artifacts
eliminated. Don’t change the
SR Frequency Weighting.
Channel selection for
processing
