ZEISS
Left Tool Area and Hardware Control Tools
ELYRA 7
190
000000-2262-999
03/2019 V_02
5.3.14.4
Localization Microscopy Tools –
Remove SMLM Outliers
The
Remove
SMLM outliers
function allows
removing all molecules that within a defined radius
will have less than the specified numbers of
neighboring molecules.
Select the
Remove SMLM outliers
tab to select
the
Remove SMLM outliers
processing tool
(Fig. 302). Activate the image you want to process
in the image container and press the
Select
button
to load the image. Then expand the
Method
Parameters
tool window to have access to the filter
functions (Fig. 303).
You can set two parameters by using the sliders or
the spin input boxes:
Radius [nm]
. The radius defines the distance from a
localized position of a peak (molecule) in which all
peaks falling within that distance are counted.
Position threshold
. If the number of counted
neighboring peaks (molecules) falls short of the set
value, the respective peak (molecule) will be
removed from the list and the SMLM image.
This tool will emphasize densely labeled
structures and can help remove floating
molecules and ghost signals.
This tool works only for SMLM images.
After setting the thresholds, press
Apply
to create
the new image. A message will be displayed telling
how many molecules have been removed from the
input SMLM image (Fig. 304).
Press
Ok
to have access to the newly computed
image (Fig. 305).
Please note that for 3D-SMLM removing
outliers applies only in 2D for a maximum
intensity projection of the Z-Stack. Removing
outliers does not apply for the z direction.
Fig. 302
Processing – Remove SMLM outliers
tool selected
Fig. 303
Processing – SMLM Remove SMLM
outliers
Fig. 304
Processing – SMLM Remove Outliers
message box
Fig. 305
SMLM images before (left) and after
(left) removal of outliers; Radius set
to 3000 and Position Threshold to 100.
Only those peaks / molecules in
denser structures remain.