Fiji tool for batch stitching of ACQUIFER Imaging Machine data

A Fiji macro toolset for batch stitching of overlapping tiled data from the ACQUIFER Imaging Machine (IM04).

Two methods are implemented:

- 3D stitching: generates multilayer tiffs for each channel of well-associated subposition and stitches them (recommended for any data with N(z-slices) > 2).

- slice-by-slice: stitches z-slices of each channel from different well-associated subposition individually (recommended for 2D data or thin z-stacks (N(z-slices) = 2)).

The macro extracts meta-information about XYZ coordinates from file name tokens, generates tile configurations and carries out Image Stitching (https://imagej.net/Image_Stitching) in Fiji.

It depends on the FIji plugin published in S. Preibisch, S. Saalfeld, P. Tomancak (2009) "Globally optimal stitching of tiled 3D microscopic image acquisitions", Bioinformatics, 25(11):1463-1465.