Zeiss LSM 880 Operating Manual page 338

ZEISS
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. 447). The radius of the circles will correspond to the
set value of the Peak mask size (Fig. 448).
Fig. 447
Fig. 448
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 PALM 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.
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CHAPTER 1 - SYSTEM OPERATION
Left Tool Area and Hardware Control Tools
Preview window of the image container for PALM processing
Preview window of the image container for PALM processing with the
Peak mask size set to 3 (left), 9 (middle) and 15 (right) pixels
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LSM 880
10/2014 V_01