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ELYRA 7
Left Tool Area and Hardware Control Tools
ZEISS
03/2019 V_02
000000-2262-999
193
The
Peak mask size
filter defines the radius in
pixel
units for a detected peak intensity that will be used
to cut out the peak and put the peak into a new coordinate system. The size will also be used when
fitting a 2D Gauss function to the intensity distribution of the peak.
If the image was selected by pressing the
Select
button, the
Preview
window of the Image in the image
container will show all identified peaks circled (Fig. 314). The radius of the circles will correspond to the
set value of the
Peak mask size
The bigger the radius the more prone are closely juxtaposed peaks to overlap. The smaller the
circles the more likely it is that one peak with a broad intensity distribution will be taken as two or
multiple peaks. The preview can be taken to decide what the best radius will be. 9 and 19 pixels
will work in > 95% of the cases for 2D and 3D SMLM experiments, respectively.
If a circle around a peak lying at the borders of the image does not fit completely within the image,
the peak is discarded.
Fig. 314
Preview window of the image container for SMLM processing
Fig. 315
Preview window of the image container for SMLM processing with the Peak
mask size set to 3 (left), 9 (middle) and 15 (right) pixels