CHAPTER 1 - SYSTEM OPERATIONLSM 880 Left Tool Area and Hardware Control Tools ZEISS10/2014 V_01 000000-2071-464 3255.4.13 Processing – StitchLicensing Instrumentstandard optional LSM ELYRA Lightsheet Z.1Tool accepts image data recorded data recorded with the acquisition tool Tile Scan(incl. combinations with other multi-dimensional acquisition tools). Images recordedin SIM mode on ELYRA (SIM data) must be processed with the tool StructuredIllumination before stitching. For optimal results, image data should have somedegree of lateral overlap. See full description of tool for details.With this function tiled images acquired withVersions of ZEN 2012 and upwards and the tilingfunction can be stitched together in 2D and 3D.Select a tiled image (or stack) with the Selectbutton (Fig. 430).The Correlation Threshold is defining theaccuracy with which the algorithm detectssimilarities in the adjacent image planes.If a 3D tile scan image has been acquired (Tile Scancombined with Z-Stack) then additional functionsfor the stitching procedure are available.Ignore z-shift will in some cases reveal betterresults for the 3D stitch. Depending on the imagedata the last step of the stitch algorithm, whichmakes a correction of the Z-Stacks in Z looking atthe overall image, can lead to unwanted shifts ofthe stacks in Z. This can be avoided when thisoption is checked.Fig. 430 Processing – Stitch, MethodParameters tool
