Zeiss Lightsheet Z.1 Operating Manual

Contents

CHAPTER 4 - SYSTEM OPERATIONCarl Zeiss Left Tool Area and Hardware Control Tools Lightsheet Z.1138 000000-1790-528 02/2013If the Fit check box is ticked and the Input 2checkbox inactive, than the software will align allchannels of Input image having the same formatto the first listed channel of the same format.Care should be taken about what channelswill be aligned and in which order theyappear. For SIM images the super resolution(SR) and the wide field (WF) channels arelisted alternatively (pair wise). Since allchannels are of the same format eachchannel (SR and WF) would be aligned tothe first SR channel, since SR channels arenormally listed before their correspondingWF channel. If this should be avoided,subsets of images containing only SR or WFchannels have to be created in theProcessing Tool Copy Subset andindependently aligned. The situation isdifferent for PALM images. The highresolution (HR) and sum wide field (SWF)channels are also listed alternatively, with theHR channels preceeding their correspondingSWF channels, however, the format of theHR channels is different to the one of theSWF channels. In this case the softwarealigns all HR channels to the first listed HRchannel, which will be the first displayedchannel, and all SWF channelsindependently to the first listed SWFchannel, which is second in the list.With the Fit check box ticked, the coefficienttable lists as the first column the Channel nameCh and as the last two columns the used Laser lineand camera channel Cam. In between are listedthe corresponding correction coefficients. Youhave the choice from the Alignment mode dropdown menu between Lateral, Affine andParabolic alignment.Fig. 221 Processing Channel Alignment tool fieldwith one input image (with SIM andpaired WF channels) selected