A PyQt4 GUI wrapped Python script to stitch MicroManager multiwell mosaiks
MicroManager has the option to generate mosaik images and to save each position of the mosaik as a separate tiff-stack. This program, Stitch Buddy, scans a directory containing OME-tiff files generated by Micrommanager and stitches all mosaiks it finds. The original purpose of the program was to automatically stitch all mosaiks in a multiwell plate. It also possible to scale down the stitched mosaik, and to retain all relevant metadata, such as pixel size, time resolution, and OME-XML data. If the image is rescaled, the imageJ-metadata is also rescaled, but currently not the OME-OXM metadata.
If the image mosaik is too large to fit in to RAM, there is an option to stitch the file frame-by-frame but this is very, very slow.
All tiff file reading/writing and metadata is handled by tifffile.py