S├ębastien Tosi
Interaction Level

This macro can stitch a (Z,T,C) data set with virtually no limit on the number of Z slices and time frames. The input to the macro is a folder with the raw tiff images (one image per file) as typically exported by motorized microscopes. These files must all be stores in the same folder and the file naming should ideally comply to OME-TIFF. The macro is however quite flexible: Only --X, --Y and --Z fields with user defined number of digits are compulsory. --T, --C and --L fields with user defined number of digits are necessary for multiple time frames / channels data sets. A compatible data set is provided as a .zip archive. Before processing it unzip it to a given location. The stitching is performed in a reference Z slice (and in a specific reference time frame and channel). The same displacements are applied to all the Z slices, time frames and channels. Before starting the batch processing a montage with the original images of the selected Z slice / time frame / channel is displayed together with the stitched image in this stack. If you are not satisfied with the result you can select another reference. The stitching is then performed time frame by time frame and slice by slice and the stitched images are exported to a single user defined output folder. The macro can also process a data set with multiple channels, the stitching is then computed once on a reference channel and then applied to the other channels.

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