Zeiss Lightsheet Z.1 Operating Manual

Contents

CHAPTER 4 - SYSTEM OPERATIONCarl Zeiss Left Tool Area and Hardware Control Tools Lightsheet Z.1130 000000-1790-528 02/2013All parameters will influence the Optical Transfer Function (OTF) used for reconstruction. The shape of theOTF in x, y is displayed in the OTF display window below the Manual selection field.The Preview tab shows the Input image and a Preview of the output image.By pressing Default the current parameter values will be stored as default values. By pressing Reuse thelast stored default values will be loaded.Pressing Attach allows parameter values to be attached to an image. In normal case if any of the SIMparameters will be changed, they will be applied accordingly for the processing, but may not be savedinto the image. Then if the image is saved, the values of the parameters applied for the image will belost. If you attach the corresponding tag to the image by pressing the Attach button parameter valuesused to process the image will be attached to the image, even if it is not explicitly saved again. They willthen be available for further processing, in particular for Batch processing.In the Output drop down menu you can set, whatkind of channels you want to display (Fig. 204). Youhave the option to display− SR-SIM + DCV + Widefield− SR-SIM + DCV− SR-SIM + Wide Field− SR-SIM.Highlight the option you want to display. Channeldesignations are as follows: SR for SR-SIM, WF forWide Field and D for Deconvolution (DCV).You can select between theoretically computed orexperimentally determined PSF by choosingTheoretical or Experimental in the PSF drop downmenu (Fig. 205). In case Experimental is selected, thePSF File button becomes available (Fig. 206). Pressingthe button will open Windows Explorer, which allowsyou to select any pre-saved Experimental PSF. The filename of the loaded file is displayed in the PSF Filedisplay window.Note, if the number of the Experimental PSFchannels is less than the number of the WF orSIM channels, the theoretical PSF will be usedfor the missing channels and a warning isgenerated. The program also checks the matchof the excitation wavelengths between the PSFand WF / SIM channels. In case of mismatching,it generates a warning, but the experimentalPSF will still be used.By pressing Apply the high resolution image will becomputed with the current parameter values(Fig. 207).If a value is changed you have the possibility to press Combine. Then a new calculation is only done forthe changed parameter and combined with the previous calculations on the unchanged parameters,which will save dramatically computational time. If Apply is pressed, calculations will be done on allparameters regardless of being changed or unchanged.Fig. 204 Output drop down menuFig. 205 PSF drop down menuFig. 206 PSF selection menuFig. 207 SIM image (left) and wide fieldimage (right) in the Split mode afterSIM processing