CHAPTER 1 - SYSTEM OPERATIONZEISS Left Tool Area and Hardware Control Tools LSM 880338 000000-2071-464 10/2014 V_015.4.14.5 PALM – Remove PALM OutliersThe Remove PALM outliers function allowsremoving all molecules that within a defined radiuswill have less than the specified numbers ofneighboring molecules.Select the Remove PALM outliers tab to selectthe Remove PALM outliers processing tool(Fig. 460). Activate the image you want to processin the image container and press the Select buttonto load the image. Then expand the MethodParameters tool window to have access to thefilter functions (Fig. 461).You can set two parameters by using the sliders orthe spin input boxes:Radius [nm]. The radius defines the distance froma localized position of a peak (molecule) in whichall peaks falling within that distance are counted.Position threshold. If the number of countedneighboring peaks (molecules) falls short of the setvalue, the respective peak (molecule) will beremoved from the list and the PALM image.This tool will emphasize densely labeledstructures and can help remove floatingmolecules and ghost signals.This tool works only for PALM images.After setting the thresholds, press Apply to createthe new image. A message will be displayed tellinghow many molecules have been removed from theinput PALM image (Fig. 462).Press Ok to have access to the newly computedimage (Fig. 463).Please note that for 3D-PALM removingoutliers applies only in 2D for a maximumintensity projection of the Z-Stack. Removingoutliers does not apply for the z direction.Fig. 460 Processing – Remove PALM outlierstool selectedFig. 461 Processing – PALM Remove PALMoutliersFig. 462 Processing – PALM Remove Outliersmessage boxFig. 463 PALM images before (left) and after(left) removal of outliers; Radius set to3000 and Position Threshold to 100.Only those peaks / molecules in denserstructures remain.
