Zeiss Lightsheet Z.1 Operating Manual

Contents

CHAPTER 4 - SYSTEM OPERATIONLightsheet Z.1 Left Tool Area and Hardware Control Tools Carl Zeiss02/2013 000000-1790-528 151Expand To Maximum Volume: This checkbox is activated as default. In a multiview experiment not allviews might include all the information. When Expand To Maximum Volume is activated, the volumeof the resulting dataset after registration and fusion is determined and additional black pixel (x,y) and z-slices are added to the views during registration. This prevents loss of data for later fusion.Scaling x=y=z: The dimensions are downsized to the smallest to have the same size.Individual Registration For Every Time point: If the multiview experiment has been performed overtime, this option becomes available.− If activated, each time point generates a transformation matrix and each time point is registeredindividually. As a result, the time necessary for registration is multiplied by the number of timepoints and can rise substantially. However, if the motorized movement of the sample by the systemhas changed (e.g. due to thermic effects on the system: not fully warmed up at start, incubation,air conditioning of the room), the Individual Registration For Every Time point option becomesnecessary.− If not activated, one transformation matrix is generated for all the following time points basedupon the first time point. As a result, processing for registration has only to be done once whichreduces processing time.Registration Options: Use Registration From FileWhen the Registration for the dataset has been determined already and the transformation matrix hasbeen saved as an .xml file (Filename.czi.xml), this option can be chosen. Click on the button next toRegistration File to open a Windows Explorer window in which you can find and select the file.With the drop down menus, the Interpolation mode and Dual Side Fusion processing can be chosen(see as well Landmark Alignment or Intensity Based Alignment section).Expand To Maximum Volume: This checkbox is activated as the default. In a multiview experiment, theZ-Stacks are often of different sizes. When Expand To Maximum Volume is activated, it will use themaximum slice number (from one View) present in the dataset for registration. The additional z-slicesneeded in other views will be filled with black frames. This will ensure that no data is lost from views withlarger z-dimensions. If this checkbox is not activated, the number of z-slices from the first View is takenas the default and larger Z-Stacks will be cut; there is a risk of data loss.Scaling x=y=z: The dimensions are downsized to the smallest to have the same size.Input settingsIn this sub-menu, a subset of a present time seriescan be chosen for the Registration and Fusionprocessing (Fig. 236).Use the two sliders or input boxes with arrows oneach side to truncate the Time points. If not everytime point in this period should be taken, theSteps can be defined with the input-box witharrows.If a subset of a time series is defined this way, the resulting images will be numbered according to theirnew sequence, which might not be the same as in the input file.Fig. 236 Processing – Lightsheet Processing.Multiview Processing, Input Settings