Zeiss Lightsheet Z.1 Operating Manual

Contents

CHAPTER 4 - SYSTEM OPERATIONCarl Zeiss Left Tool Area and Hardware Control Tools Lightsheet Z.1156 000000-1790-528 02/20133.3.19.1 Remove Structure• Activate Remove structures in the ICS tool. TheRemove structures menu will appear.• To select an image, highlight the image in the imagecontainer and press the Select button. This will beyour Input image.As an output image an image with the selected averagesubtracted is computed and the result presented in thePreview window.• If the Apply button is pressed, the averagedsubtracted image stack will be opened as a newimage in the container.You have four options that can be selected via the Remove Structures drop down menu (Fig. 243):None, Slowly moving structure, Immobile structures (+Stack) and Immobile structures (+Plane).If None is selected, no average will be subtracted and the original image is kept. If Slowly movingstructure is activated the Average frames input box becomes available. Type in the required number(minimum is 2) or use the slider or arrows for input. The number defines the number of frames that willbe averaged and subtracted in a gliding way from the original stack in the following way:• From a stack of n frames take successive m moving average frames with an overlap of m-1 andaverage these. The outcome is a new stack with n-m+1 gliding or moving average frames. Calculatefrom each of the average frames the overall average of all pixels, which is a scalar.• Subtract the i-th of the gliding average frame from the (i-1)+m/2 original frame and add the i-thscalar. In this way, the first frame to be used from the original stack is m/2 and the last m/2+(n-m+1).This creates a new stack of n-m-1 frames that is the output image.If Immobile structures (+Stack) is selected, the average frame of the stack will be computed andsubtracted from each original frame. This creates a new average subtracted stack of the same size. Anaverage value of all pixels from all frames is computed, which is a scalar, and added to each pixel of thesingle frames of the average subtracted stack to avoid negative numbers. The resulting stack is theoutput image.If Immobile structures (+Plane) is selected, the average frame of the stack will be computed andsubtracted from each original frame. This creates a new average subtracted stack of the same size.Average values of all pixels from each of the original frames is computed, which is a scalar, and added toeach pixel of each corresponding single frame of the average subtracted stack to avoid negativenumbers. The resulting stack is the output image.Fig. 243 Remove structure drop downmenu