Zeiss LSM 880, Operating Manual

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CHAPTER 1 - SYSTEM OPERATION
ZEISS Left Tool Area and Hardware Control Tools LSM 880
332 000000-2071-464 10/2014 V_01
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).
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.
Fig. 447 Preview window of the image container for PALM processing
Fig. 448 Preview window of the image container for PALM processing with the
Peak mask size set to 3 (left), 9 (middle) and 15 (right) pixels